Exon 10 skipping in ACAT1 caused by a novel c.949G>A mutation located at an exonic splice enhancer site

Mol Med Rep. 2016 Nov;14(5):4906-4910. doi: 10.3892/mmr.2016.5819. Epub 2016 Oct 10.


Beta-ketothiolase deficiency, also known as mitochondrial acetoacetyl-CoA thiolase (T2) deficiency, is an autosomal recessive disease caused by mutations in the acetyl‑CoA acetyltransferase 1 (ACAT1) gene. A German T2‑deficient patient that developed a severe ketoacidotic episode at the age of 11 months, was revealed to be a compound heterozygote of a previously reported null mutation, c.472A>G (p.N158D) and a novel mutation, c.949G>A (p.D317N), in ACAT1. The c.949G>A mutation was suspected to cause aberrant splicing as it is located within an exonic splicing enhancer sequence (c. 947CTGACGC) that is a potential binding site for serine/arginine‑rich splicing factor 1. A mutation in this sequence, c.951C>T, results in exon 10 skipping. A minigene construct was synthesized that included exon 9‑truncated intron 9‑exon 10‑truncated intron 10‑exon 11, and the splicing of this minigene revealed that the c.949G>A mutant construct caused exon 10 skipping in a proportion of the transcripts. Furthermore, additional substitution of G for C at the first nucleotide of exon 10 (c.941G>C) abolished the effect of the c.949G>A mutation. Transient expression analysis of the c.949G>A mutant cDNA revealed no residual T2 activity in the mutated D317N enzyme. Therefore, c.949G>A (D317N) is a pathogenic missense mutation, and diminishes the effect of an exonic splicing enhancer and causes exon 10 skipping. The present study demonstrates that a missense mutation, or even a synonymous substitution, may disrupt enzyme function by interference with splicing.

Publication types

  • Case Reports

MeSH terms

  • Acetyl-CoA C-Acetyltransferase / genetics*
  • Acetyl-CoA C-Acyltransferase / deficiency
  • Acetyl-CoA C-Acyltransferase / genetics
  • Alternative Splicing*
  • Amino Acid Metabolism, Inborn Errors / diagnosis
  • Amino Acid Metabolism, Inborn Errors / genetics
  • Base Sequence
  • Enhancer Elements, Genetic
  • Enzyme Activation
  • Exons*
  • Female
  • Gene Expression
  • Humans
  • Infant
  • Mutation*
  • Mutation, Missense
  • RNA Splice Sites*


  • RNA Splice Sites
  • Acetyl-CoA C-Acyltransferase
  • ACAT1 protein, human
  • Acetyl-CoA C-Acetyltransferase

Supplementary concepts

  • Beta ketothiolase deficiency